AGBU, A Joint Venture of NSW Department of Primary Industries and University of New England, Armidale, NSW, 2351, Australia.
Genet Sel Evol. 2023 Jan 25;55(1):7. doi: 10.1186/s12711-023-00781-7.
Restricted maximum likelihood estimation of genetic parameters accounting for genomic relationships has been reported to impose computational burdens which typically are many times higher than those of corresponding analyses considering pedigree based relationships only. This can be attributed to the dense nature of genomic relationship matrices and their inverses. We outline a reparameterisation of the multivariate linear mixed model to principal components and its effects on the sparsity pattern of the pertaining coefficient matrix in the mixed model equations. Using two data sets we demonstrate that this can dramatically reduce the computing time per iterate of the widely used 'average information' algorithm for restricted maximum likelihood. This is primarily due to the fact that on the principal component scale, the first derivatives of the coefficient matrix with respect to the parameters modelling genetic covariances between traits are independent of the relationship matrix between individuals, i.e. are not afflicted by a multitude of genomic relationships.
已有研究报告称,考虑到基因组关系,对遗传参数进行限制最大似然估计会带来计算负担,通常比仅考虑基于系谱关系的分析高出许多倍。这归因于基因组关系矩阵及其逆的密集性质。我们概述了多元线性混合模型向主成分的重新参数化及其对混合模型方程中相关系数矩阵稀疏模式的影响。使用两个数据集,我们证明这可以极大地减少广泛使用的“平均信息”算法对限制最大似然的每次迭代的计算时间。这主要是因为在主成分尺度上,关于性状间遗传协方差建模的参数的系数矩阵的一阶导数与个体之间的关系矩阵无关,即不受众多基因组关系的影响。